Andrews S 2010 FastQC: A quality control tool for high throughput sequence data (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Anwar SL, Wulaningsih W and Lehmann U 2017 Transposable elements in human cancer: Causes and consequences of deregulation. Int. J. Mol. Sci. 18 974
Article PubMed PubMed Central Google Scholar
Armstrong RA 2019 Risk factors for Alzheimer’s disease. Folia Neuropathol. 57 87–105
Bao W, Kojima KK and Kohany O 2015 Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob. DNA 6 11
Article PubMed PubMed Central Google Scholar
Billingsley KJ, Lättekivi F, Planken A, et al. 2019 Analysis of repetitive element expression in the blood and skin of patients with Parkinson’s disease identifies differential expression of satellite elements. Sci. Rep. 9 4369
Article PubMed PubMed Central Google Scholar
Boccardi V, Comanducci C, Baroni M, et al. 2017 Of energy and entropy: the ineluctable impact of aging in old age dementia. Int. J. Mol. Sci. 18 2672
Article PubMed PubMed Central Google Scholar
Bolger AM, Lohse M and Usadel B 2014 Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 2114–2120
Article PubMed PubMed Central Google Scholar
Bollati V, Galimberti D, Pergoli L, et al. 2011 DNA methylation in repetitive elements and Alzheimer disease. Brain Behav. Immun. 25 1078–1083
Article PubMed PubMed Central Google Scholar
Burns KH 2017 Transposable elements in cancer. Nat. Rev. Cancer 17 415–424
Colombo AR, Elias HK and Ramsingh G 2018 Senescence induction universally activates transposable element expression. Cell Cycle 17 1846–1857
Article PubMed PubMed Central Google Scholar
Criscione SW, Zhang Y, Thompson W, et al. 2014 Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC Genomics 15 583
Article PubMed PubMed Central Google Scholar
De Cecco M, Ito T, Petrashen AP, et al. 2019 L1 drives IFN in senescent cells and promotes age-associated inflammation. Nature 566 73–78
Article PubMed PubMed Central Google Scholar
Evering TH, Marston JL, Gan L, et al. 2023 Transposable elements and Alzheimer’s disease pathogenesis. Trends Neurosci. 46 170–172
Frankish A, Diekhans M, Jungreis I, et al. 2021 GENCODE 2021. Nucleic Acids Res. 49 D916–D923
Frisoni GB, Altomare D, Thal DR, et al. 2022 The probabilistic model of Alzheimer disease: the amyloid hypothesis revised. Nat. Rev. Neurosci. 23 53–66
Fueyo R, Judd J, Feschotte C, et al. 2022 Roles of transposable elements in the regulation of mammalian transcription. Nat. Rev. Mol. Cell Biol. 23 481–497
Article PubMed PubMed Central Google Scholar
Ge SX, Jung D and Yao R 2020 ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 36 2628–2629
Goenka A, Sengupta S, Pandey R, et al. 2016 Human satellite-III non-coding RNAs modulate heat-shock-induced transcriptional repression. J. Cell Sci. 129 3541–3552
Golkaram M, Salmans ML, Kaplan S, et al. 2021 HERVs establish a distinct molecular subtype in stage II/III colorectal cancer with poor outcome. NPJ Genom. Med. 6 13
Article PubMed PubMed Central Google Scholar
Gorbunova V, Seluanov A, Mita P, et al. 2021 The role of retrotransposable elements in ageing and age-associated diseases. Nature 596 43–53
Article PubMed PubMed Central Google Scholar
Gräff J and Tsai L-H 2013 Histone acetylation: molecular mnemonics on the chromatin. Nat. Rev. Neurosci. 14 97–111
Gröger V and Cynis H 2018 Human endogenous retroviruses and their putative role in the development of autoimmune disorders such as multiple sclerosis. Front. Microbiol. 9 265
Article PubMed PubMed Central Google Scholar
Guo C, Jeong H-H, Hsieh Y-C, et al. 2018 Tau activates transposable elements in Alzheimer’s disease. Cell Rep. 23 2874–2880
Article PubMed PubMed Central Google Scholar
Hall LL, Byron M, Carone DM, et al. 2017 Demethylated HSATII DNA and HSATII RNA foci sequester PRC1 and MeCP2 into cancer-specific nuclear bodies. Cell Rep. 18 2943–2956
Article PubMed PubMed Central Google Scholar
Hancks DC and Kazazian HH 2016 Roles for retrotransposon insertions in human disease. Mob. DNA 7 9
Article PubMed PubMed Central Google Scholar
Heinz S, Benner C, Spann N, et al. 2010 Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38 576–589
Article PubMed PubMed Central Google Scholar
Huber W, Carey VJ, Gentleman R, et al. 2015 Orchestrating high-throughput genomic analysis with bioconductor. Nat. Methods 12 115–121
Article PubMed PubMed Central Google Scholar
Jachowicz JW, Santenard A, Bender A, et al. 2013 Heterochromatin establishment at pericentromeres depends on nuclear position. Genes Dev. 27 2427–2432
Article PubMed PubMed Central Google Scholar
Janota I and Mountjoy CQ 1988 Asymmetry of pathology in Alzheimer’s disease. J. Neurol. Neurosurg. Psychiatry 51 1011–1012
Article PubMed PubMed Central Google Scholar
Kaikkonen MU, Lam MTY and Glass CK 2011 Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc. Res. 90 430–440
Article PubMed PubMed Central Google Scholar
Kapoor A and Nation DA 2021 Role of Notch signaling in neurovascular aging and Alzheimer’s disease. Semin. Cell Dev. Biol. 116 90–97
Karakülah G and Yandim C 2020 Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence. Turk. J. Biol. Turk. Biyol. Derg. 44 356–370
Langfelder P and Horvath S 2008 WGCNA: An R package for weighted correlation network analysis. BMC Bioinform. 9 559
Langfelder P, Zhang B and Horvath S 2008 Defining clusters from a hierarchical cluster tree: The Dynamic Tree Cut package for R. Bioinform. 24 719–720
Langmead B and Salzberg SL 2012 Fast gapped-read alignment with Bowtie 2. Nat. Methods 9 357–359
Article PubMed PubMed Central Google Scholar
LaRocca TJ, Cavalier AN and Wahl D 2020 Repetitive elements as a transcriptomic marker of aging: Evidence in multiple datasets and models. Aging Cell 19 e13167
Comments (0)